Publications

Abstract (Expand)

Organisms use circadian clocks to generate 24-h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these ...

Authors: Bruno MC Martins, Arijit K Das, Liliana Antunes, James CW Locke

Date Published: 22nd Dec 2016

Journal: Mol Syst Biol

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. ...

Authors: Katy Wolstencroft, Olga Krebs, Jacky Snoep, Natalie Stanford, Finn Bacall, Martin Golebiewski, Rostyslav Kuzyakiv, Quyen Nguyen, Stuart Owen, S. Soiland-Reyes, Jakub Straszewski, D. D. van Niekerk, Alan Williams, L. Malmstrom, Bernd Rinn, Wolfgang Müller, Carole Goble

Date Published: 3rd Dec 2016

Journal: Nucleic Acids Res

Abstract (Expand)

Wild-type Corynebacterium glutamicum has no endogenous metabolic activity for utilizing the lignocellulosic pentose d-xylose for cell growth. Therefore, two different engineering approaches have been ...

Authors: A. Radek, M. F. Muller, J. Gatgens, L. Eggeling, K. Krumbach, J. Marienhagen, Stephan Noack

Date Published: 15th Jun 2016

Journal: J Biotechnol

Abstract (Expand)

The intra- and extracellular concentrations of 16 metabolites were measured in chemostat (D = 0.1 h−1) anaerobic cultures of the yeast Saccharomyces cerevisiae CEN.PK-113-7D growing on minimal medium. ...

Authors: Maksim Zakhartsev, Oliver Vielhauer, Thomas Horn, Xuelian Yang, Matthias Reuss

Date Published: 1st Apr 2015

Journal: Metabolomics

Abstract (Expand)

BACKGROUND AIMS: Mesenchymal stromal cells (MSCs) resemble an essential component of the bone marrow niche for maintenance of stemness of hematopoietic progenitor cells (HPCs). Perturbation of the C-X-C ...

Authors: A. Ludwig, Rainer Saffrich, V. Eckstein, T. Bruckner, W. Wagner, A. D. Ho, P. Wuchter

Date Published: 10th Oct 2013

Journal: Cytotherapy

Abstract (Expand)

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original ...

Authors: Franco Du Preez, David D van Niekerk, Bob Kooi, Johann M Rohwer, Jacky Snoep

Date Published: 21st Jun 2012

Journal: The FEBS journal

Abstract (Expand)

In an accompanying paper [du Preez et al., (2012) FEBS J doi: 10.1111/j.1742-4658.2012.08665.x], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. ...

Authors: Franco Du Preez, David D van Niekerk, Jacky Snoep

Date Published: 13th Jun 2012

Journal: The FEBS journal

Abstract (Expand)

Pausing of transcription is an important step of regulation of gene expression in bacteria and eukaryotes. Here we uncover a factor-independent mechanism of transcription pausing, which is determined ...

Authors: Aleksandra Bochkareva, Yulia Yuzenkova, Vasisht R Tadigotla, Nikolay Zenkin

Date Published: 29th Nov 2011

Journal: EMBO J.

Abstract (Expand)

Sortases of Gram-positive bacteria catalyze the covalent C-terminal anchoring of proteins to the cell wall. Bacillus subtilis, a well-known host organism for protein production, contains two putative ...

Authors: Hamidreza Fasehee, Helga Westers, Albert Bolhuis, Haike Antelmann, Michael Hecker, Wim J Quax, Agha F Mirlohi, Jan Maarten Van Dijl, Gholamreza Ahmadian

Date Published: 31st Aug 2011

Journal: Proteomics

Abstract (Expand)

The cold stress response of Pseudomonas putida KT2440 was investigated by genomewide deep cDNA sequencing and gel-free MS-based protein profiling. Transcriptome and proteome profiles were assessed at ...

Authors: Sarah Frank, F. Schmidt, Jens Klockgether, C. F. Davenport, M. Gesell Salazar, U. Volker, Burkhard Tuemmler

Date Published: 1st Mar 2011

Journal: FEMS Microbiol Lett

Abstract (Expand)

Any signal transduction requires communication between a sensory component and an effector. Some enzymes engage in signal perception and transduction, as well as in catalysis, and these proteins are ...

Authors: Katrin Gunka, Joseph Newman, Fabian M Commichau, Christina Herzberg, Cecilia Rodrigues, Lorraine Hewitt, Rick Lewis, Jörg Stülke

Date Published: 22nd Feb 2010

Journal: J. Mol. Biol.

Abstract (Expand)

Pseudomonas putida DOT-T1E is a highly solvent-tolerant strain. Although the main mechanism that confers solvent tolerance to the strain is the TtgGHI efflux pump, a number of other proteins are also ...

Authors: Vanina García, Patricia Godoy, Craig Daniels, Ana Hurtado, Juan Ramos, Ana Segura

Date Published: 1st Nov 2009

Journal: Not specified

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we ...

Authors: F. B. du Preez, Dawie Van Niekerk, Jacky Snoep

Date Published: No date defined

Journal: FEBS J

Abstract (Expand)

UNLABELLED: An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the ...

Authors: F. B. du Preez, Dawie Van Niekerk, B. Kooi, J. M. Rohwer, Jacky Snoep

Date Published: No date defined

Journal: FEBS J

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